Merge branch 'release-0.7.0' into 'master'
Release 0.7.0 See merge request !449
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- .gitignore .gitignore +0 -2
- LICENSE LICENSE +0 -0
- README.md README.md +4 -4
- bam2wig/.gitignore bam2wig/.gitignore +0 -0
- bam2wig/pom.xml bam2wig/pom.xml +61 -0
- bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala ...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala +75 -0
- bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala ...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala +47 -0
- bam2wig/src/test/resources/empty.bam bam2wig/src/test/resources/empty.bam +0 -0
- bam2wig/src/test/resources/log4j.properties bam2wig/src/test/resources/log4j.properties +24 -0
- bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala ...sc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala +44 -0
- bammetrics/.gitignore bammetrics/.gitignore +0 -0
- bammetrics/pom.xml bammetrics/pom.xml +58 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp ...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp +103 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp ...lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp ...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp .../sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp ...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp ...nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp ...urces/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp ...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp ...esources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp ...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py ...biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py +320 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp ...urces/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp +0 -0
- bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp ...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp +0 -0
- bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala ...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala +201 -0
- bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala ...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +432 -0
- bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala ...lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala +30 -0
- bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala ...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala +63 -0
- bammetrics/src/test/resources/log4j.properties bammetrics/src/test/resources/log4j.properties +24 -0
- bammetrics/src/test/resources/ref.dict bammetrics/src/test/resources/ref.dict +0 -0
- bammetrics/src/test/resources/ref.fa bammetrics/src/test/resources/ref.fa +0 -0
- bammetrics/src/test/resources/ref.fa.fai bammetrics/src/test/resources/ref.fa.fai +0 -0
- bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala ...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala +123 -0
- basty/.gitignore basty/.gitignore +0 -0
- basty/pom.xml basty/pom.xml +58 -0
- basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala ...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala +199 -0
- basty/src/test/resources/log4j.properties basty/src/test/resources/log4j.properties +24 -0
- biopet-aggregate/pom.xml biopet-aggregate/pom.xml +40 -25
- biopet-core/pom.xml biopet-core/pom.xml +79 -0
- biopet-core/src/main/resources/log4j.properties biopet-core/src/main/resources/log4j.properties +25 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt ...t-core/src/main/resources/nl/lumc/sasc/biopet/License.txt +12 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp ...resources/nl/lumc/sasc/biopet/core/report/executables.ssp +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css ...c/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css +1 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css ...nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css +1 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css ...c/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css +179 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css ...c/biopet/core/report/ext/css/sortable-theme-bootstrap.css +104 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.ttf ...et/core/report/ext/fonts/glyphicons-halflings-regular.ttf +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff ...t/core/report/ext/fonts/glyphicons-halflings-regular.woff +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff2 .../core/report/ext/fonts/glyphicons-halflings-regular.woff2 +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js ...s/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js +2 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/d3.v3.5.5.min.js ...s/nl/lumc/sasc/biopet/core/report/ext/js/d3.v3.5.5.min.js +5 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js ...rces/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js +4 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js ...es/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js +2 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp .../main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp ...sources/nl/lumc/sasc/biopet/core/report/librariesList.ssp +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp ...c/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp ...n/resources/nl/lumc/sasc/biopet/core/report/reference.ssp +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp ...resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R ...rc/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R ...resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R ...main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R +0 -0
- biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R .../resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R +0 -0
- biopet-core/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R ...urces/org/broadinstitute/gatk/queue/util/queueJobReport.R +0 -0
- biopet-core/src/main/resources/picard/analysis/baseDistributionByCycle.R .../main/resources/picard/analysis/baseDistributionByCycle.R +0 -0
- biopet-core/src/main/resources/picard/analysis/gcBias.R biopet-core/src/main/resources/picard/analysis/gcBias.R +0 -0
- biopet-core/src/main/resources/picard/analysis/insertSizeHistogram.R .../src/main/resources/picard/analysis/insertSizeHistogram.R +0 -0
- biopet-core/src/main/resources/picard/analysis/meanQualityByCycle.R ...e/src/main/resources/picard/analysis/meanQualityByCycle.R +0 -0
- biopet-core/src/main/resources/picard/analysis/qualityScoreDistribution.R ...main/resources/picard/analysis/qualityScoreDistribution.R +0 -0
- biopet-core/src/main/resources/picard/analysis/rnaSeqCoverage.R ...-core/src/main/resources/picard/analysis/rnaSeqCoverage.R +0 -0
- biopet-core/src/main/resources/picard/analysis/rrbsQc.R biopet-core/src/main/resources/picard/analysis/rrbsQc.R +0 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala .../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala +282 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala .../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala +173 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala ...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala +68 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala .../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala +88 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala ...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala +156 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala ...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala +118 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala ...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala +252 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala ...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala +101 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala ...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala +172 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala ...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala +40 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala .../nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala +23 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala .../scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala +31 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala ...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala +92 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala ...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala +133 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala ...la/nl/lumc/sasc/biopet/core/annotations/Annotations.scala +61 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala ...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala +49 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala ...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala +57 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala ...sc/biopet/core/extensions/PythonCommandLineFunction.scala +62 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala ...c/biopet/core/extensions/RscriptCommandLineFunction.scala +36 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala ...mc/sasc/biopet/core/report/MultisampleReportBuilder.scala +64 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala ...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala +268 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala ...in/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala +26 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala ...scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala +33 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala ...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala +45 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala ...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala +174 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala ...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala +196 -0
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala ...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala +326 -0
- biopet-core/src/test/resources/empty_summary.json biopet-core/src/test/resources/empty_summary.json +0 -0
- biopet-core/src/test/resources/fake_chrQ.dict biopet-core/src/test/resources/fake_chrQ.dict +0 -0
- biopet-core/src/test/resources/fake_chrQ.fa biopet-core/src/test/resources/fake_chrQ.fa +0 -0
- biopet-core/src/test/resources/fake_chrQ.fa.fai biopet-core/src/test/resources/fake_chrQ.fa.fai +0 -0
- biopet-core/src/test/resources/fake_chrQ_no_index.fa biopet-core/src/test/resources/fake_chrQ_no_index.fa +0 -0
- biopet-core/src/test/resources/log4j.properties biopet-core/src/test/resources/log4j.properties +24 -0
- biopet-core/src/test/resources/template.ssp biopet-core/src/test/resources/template.ssp +0 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala .../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala +59 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala ...a/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala +89 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala ...ala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala +246 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala .../scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala +43 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala ...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala +93 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala ...scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala +55 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala ...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala +44 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala ...cala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala +74 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala ...asc/biopet/core/report/MultisampleReportBuilderTest.scala +60 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala ...a/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala +89 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala ...a/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala +31 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala ...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala +46 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala ...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala +140 -0
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala ...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala +360 -0
- biopet-extensions/pom.xml biopet-extensions/pom.xml +57 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py ...umc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py +196 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R ...rc/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R +68 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops_wes.R ...ain/resources/nl/lumc/sasc/biopet/extensions/cnmops_wes.R +77 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R ...rces/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R +76 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R ...rces/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R +211 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/freec/freec_assess_significance.R .../sasc/biopet/extensions/freec/freec_assess_significance.R +71 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py ...lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py +33 -0
- biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py ...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py +53 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala ...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala +55 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala +39 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala ...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala +62 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala +58 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala +235 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala +149 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala +37 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala .../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala +288 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala +98 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala +119 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala +205 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala +64 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala .../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala +54 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala +49 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala +90 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala ...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala +123 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala +62 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala +73 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala +116 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala +85 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala ...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala +45 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala +137 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala ...c/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala +186 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala +107 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala +437 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala +117 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala +47 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala +370 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala .../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala +311 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala ...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala +55 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala +62 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala ...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala +25 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala ...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala +86 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala .../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala +63 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala ...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala +198 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala ...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala +25 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala ...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala +100 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala ...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala +87 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala ...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala +71 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala .../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala +42 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala ...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala +41 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala .../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala +98 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala ...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala +254 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala .../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala +51 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala ...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala +51 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala ...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala +105 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala ...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala +74 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala ...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala +51 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala ...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala +30 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala +100 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala ...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala +58 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala +115 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala ...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala +81 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala ...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala +59 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala .../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala +87 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala .../nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala +149 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala ...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala +33 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala .../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala +47 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala .../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala +34 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala ...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala +38 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala .../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala +39 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala ...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala +54 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala ...in/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala +213 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala ...biopet/extensions/freec/FreeCAssessSignificancePlot.scala +46 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala ...a/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala +42 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala ...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala +40 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala .../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala +81 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala ...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala +118 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala .../lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala +47 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala ...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala +197 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala ...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala +77 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala .../lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala +52 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala ...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala +103 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala ...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala +142 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala ...nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala +420 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ContigScatterFunction.scala ...c/sasc/biopet/extensions/gatk/ContigScatterFunction.scala +38 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala ...umc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala +109 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala ...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala +135 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala ...a/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala +159 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala ...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala +525 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala .../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala +193 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala ...mc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala +33 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala ...cala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala +112 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala .../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala +97 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala .../nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala +276 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala ...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala +336 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala ...l/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala +137 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala ...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala +175 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala ...umc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala +227 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala ...scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala +59 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala +441 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala ...n/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala +259 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala ...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala +96 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala ...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala +30 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala .../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala +124 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala .../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala +77 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala .../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala +53 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala ...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala +29 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala .../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala +118 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala ...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala +97 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala .../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala +46 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala .../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala +46 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala ...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala +41 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala ...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala +33 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala ...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala +37 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala ...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala +36 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala ...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala +36 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala ...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala +44 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala ...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala +40 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala ...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala +76 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala .../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala +52 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala .../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala +55 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala .../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala +43 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala .../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala +36 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala ...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala +93 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala ...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala +53 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala ...nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala +38 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala ...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala +90 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala ...et/extensions/picard/CollectAlignmentSummaryMetrics.scala +86 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala .../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala +91 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala ...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala +91 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala ...asc/biopet/extensions/picard/CollectMultipleMetrics.scala +134 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala .../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala +106 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala .../biopet/extensions/picard/CollectTargetedPcrMetrics.scala +93 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala ...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala +82 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala ...c/biopet/extensions/picard/CreateSequenceDictionary.scala +46 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala ...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala +35 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala ...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala +115 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala ...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala +77 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala .../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala +165 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala ...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala +58 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala ...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala +103 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala ...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala +61 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala ...scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala +60 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala .../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala +219 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala .../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala +96 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala ...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala +108 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala ...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala +101 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala ...a/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala +55 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala ...nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala +52 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala ...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala +79 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala .../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala +88 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala ...scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala +168 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala ...ala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala +59 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala ...mc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala +98 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala ...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala +30 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala ...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala +39 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala .../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala +59 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala ...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala +66 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala .../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala +42 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala ...umc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala +42 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala ...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala +47 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala .../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala +26 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala ...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala +26 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala .../lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala +48 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala ...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala +41 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala ...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala +84 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala ...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala +51 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala ...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala +69 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala ...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala +26 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala ...la/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala +47 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala ...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala +125 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala ...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala +26 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala ...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala +28 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala ...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala +64 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala +27 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala ...scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala +46 -0
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala ...scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala +54 -0
- biopet-extensions/src/test/resources/log4j.properties biopet-extensions/src/test/resources/log4j.properties +24 -0
- biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/expectedresult.clever.vcf ...c/sasc/biopet/extensions/clever/expectedresult.clever.vcf +43 -0
- biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/test.clever.vcf ...ces/nl/lumc/sasc/biopet/extensions/clever/test.clever.vcf +4 -0
- biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics ...umc/sasc/biopet/extensions/picard/picard.alignmentMetrics +0 -0
- biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics ...l/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics +0 -0
- biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics ...mc/sasc/biopet/extensions/picard/picard.insertsizemetrics +0 -0
- biopet-extensions/src/test/resources/ref.fa.fai biopet-extensions/src/test/resources/ref.fa.fai +1 -0
- biopet-extensions/src/test/resources/vep.failed.metrics biopet-extensions/src/test/resources/vep.failed.metrics +36 -0
- biopet-extensions/src/test/resources/vep.metrics biopet-extensions/src/test/resources/vep.metrics +0 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala ...t/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala +49 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala ...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala +49 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala ...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala +51 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala ...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala +43 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala ...rc/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala +125 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala ...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala +386 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala ...c/sasc/biopet/extensions/VariantEffectPredictorTest.scala +72 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala ...lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala +96 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala ...xtensions/picard/CollectAlignmentSummaryMetricsTest.scala +39 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala ...opet/extensions/picard/CollectInsertSizeMetricsTest.scala +39 -0
- biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala ...mc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala +39 -0
- biopet-package/.gitignore biopet-package/.gitignore +0 -0
- biopet-package/pom.xml biopet-package/pom.xml +161 -0
- biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala ...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala +45 -0
- biopet-package/src/test/resources/log4j.properties biopet-package/src/test/resources/log4j.properties +24 -0
- biopet-tools-extensions/pom.xml biopet-tools-extensions/pom.xml +66 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala ...la/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala +105 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala ...umc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala +69 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala .../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala +51 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala ...sc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala +37 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala ...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala +57 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala .../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala +42 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala +103 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala +76 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala +55 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala ...umc/sasc/biopet/extensions/tools/KrakenReportToJson.scala +69 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala ...a/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala +58 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala ...a/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala +44 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala ...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala +99 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala ...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala +77 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala ...la/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala +67 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala ...nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala +37 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala ...lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala +53 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala ...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala +53 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala .../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala +78 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala ...a/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala +55 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala +41 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala .../nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala +37 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala +86 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala ...scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala +115 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala ...ala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala +62 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala .../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala +52 -0
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala +86 -0
- biopet-tools-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala .../nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala +155 -0
- biopet-tools-package/pom.xml biopet-tools-package/pom.xml +77 -0
- biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala ...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala +52 -0
- biopet-tools/pom.xml biopet-tools/pom.xml +71 -0
- biopet-tools/src/main/resources/log4j.properties biopet-tools/src/main/resources/log4j.properties +25 -0
- biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R ...rc/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R +0 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala .../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala +127 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala ...rc/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala +445 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala .../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala +254 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala .../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala +86 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala .../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala +62 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala ...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala +184 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala ...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala +284 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala .../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala +69 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala .../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala +178 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala ...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala +155 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala .../src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala +180 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala .../src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala +122 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala .../scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala +185 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala ...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala +111 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala ...c/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala +69 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala ...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala +224 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala ...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala +197 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala ...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala +81 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala .../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala +151 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala ...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala +71 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala ...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala +171 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala ...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala +129 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala ...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala +104 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala ...ls/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala +276 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala ...c/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala +140 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala .../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala +71 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala ...c/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala +109 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala .../main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala +197 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala .../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala +414 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala ...s/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala +740 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala ...s/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala +199 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala ...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala +210 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala .../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala +247 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala .../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala +425 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala ...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala +215 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala .../scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala +62 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala ...main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala +61 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala ...a/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala +81 -0
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala ...l/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala +227 -0
- biopet-tools/src/test/resources/README.txt biopet-tools/src/test/resources/README.txt +30 -0
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- biopet-tools/src/test/resources/chrQ.refflat biopet-tools/src/test/resources/chrQ.refflat +0 -0
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- biopet-tools/src/test/resources/fake_chrQ.fa biopet-tools/src/test/resources/fake_chrQ.fa +0 -0
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- biopet-tools/src/test/resources/flagstat_crosstrue.txt biopet-tools/src/test/resources/flagstat_crosstrue.txt +0 -0
- biopet-tools/src/test/resources/flagstat_report.txt biopet-tools/src/test/resources/flagstat_report.txt +0 -0
- biopet-tools/src/test/resources/flagstat_summary.txt biopet-tools/src/test/resources/flagstat_summary.txt +17 -0
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- biopet-tools/src/test/resources/log4j.properties biopet-tools/src/test/resources/log4j.properties +24 -0
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- biopet-tools/src/test/resources/rrna02.bed biopet-tools/src/test/resources/rrna02.bed +0 -0
- biopet-tools/src/test/resources/sageAllGenesTest.tsv biopet-tools/src/test/resources/sageAllGenesTest.tsv +0 -0
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- biopet-tools/src/test/resources/sageTest.tsv biopet-tools/src/test/resources/sageTest.tsv +0 -0
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- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala ...la/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala +58 -0
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- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala .../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala +85 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala ...a/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala +273 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala ...t/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala +54 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala .../test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala +309 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala ...ala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala +79 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala .../test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala +62 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala .../test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala +100 -0
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- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala ...est/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala +63 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala .../scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala +45 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala ...cala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala +134 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala ...a/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala +89 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala ...cala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala +97 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala ...rc/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala +134 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SnptestToVcfTest.scala ...st/scala/nl/lumc/sasc/biopet/tools/SnptestToVcfTest.scala +57 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala ...st/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala +88 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala ...t/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala +137 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala .../test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala +247 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala ...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala +413 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala ...c/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala +91 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala ...test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala +197 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala ...t/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala +145 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala .../test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala +546 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala ...ala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala +53 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala ...scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala +95 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala ...la/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala +73 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala .../scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala +63 -0
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstatTest.scala .../lumc/sasc/biopet/tools/flagstat/BiopetFlagstatTest.scala +77 -0
- biopet-utils/pom.xml biopet-utils/pom.xml +92 -0
- biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R ...resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R +0 -0
- biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R ...main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R +0 -0
- biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R .../resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R +0 -0
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/package.scala ...et-utils/src/main/scala/nl/lumc/sasc/biopet/package.scala +42 -0
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- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala ...in/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala +132 -0
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- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala ...ls/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala +62 -0
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala ...rc/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala +26 -0
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- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala ...s/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala +143 -0
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala .../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala +314 -0
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- gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala .../nl/lumc/sasc/biopet/pipelines/gwastest/impute/Spec.scala +78 -0
- gwas-test/src/test/resources/fake_chrQ.dict gwas-test/src/test/resources/fake_chrQ.dict +2 -0
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- gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala ...nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala +86 -0
- gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala ...asc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala +103 -0
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- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala .../sasc/biopet/pipelines/kopisu/methods/ConiferMethod.scala +76 -0
- kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala ...mc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala +71 -0
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- protected/LICENSE protected/LICENSE +0 -1
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- protected/biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt ...nsions/src/main/resources/nl/lumc/sasc/biopet/License.txt +0 -3
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala ...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala +0 -23
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala ...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala +0 -44
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala .../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala +0 -25
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala ...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala +0 -23
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala ...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala +0 -23
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala ...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala +0 -46
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala ...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala +0 -76
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala ...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala +0 -31
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala ...l/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala +0 -23
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala ...biopet/extensions/gatk/broad/RealignerTargetCreator.scala +0 -25
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala ...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala +0 -23
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala .../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala +0 -57
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala .../sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala +0 -25
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala .../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala +0 -38
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala ...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala +0 -46
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- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala ...iopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala +0 -22
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala ...pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala +0 -23
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- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala ...opet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala +0 -21
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala ...ipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala +0 -23
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- protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala .../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala +0 -147
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- public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt ...t-core/src/main/resources/nl/lumc/sasc/biopet/License.txt +0 -13
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- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala ...in/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala +0 -27
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala ...scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala +0 -34
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala ...scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala +0 -46
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala ...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala +0 -175
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala ...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala +0 -197
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala ...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala +0 -327
- public/biopet-core/src/test/resources/log4j.properties public/biopet-core/src/test/resources/log4j.properties +0 -25
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala .../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala +0 -60
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala ...a/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala +0 -90
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala ...ala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala +0 -247
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala .../scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala +0 -44
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala ...c/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala +0 -94
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala ...scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala +0 -56
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala ...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala +0 -45
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala ...asc/biopet/core/report/MultisampleReportBuilderTest.scala +0 -61
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala ...a/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala +0 -90
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala ...a/nl/lumc/sasc/biopet/core/report/ReportSectionTest.scala +0 -32
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala ...a/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala +0 -47
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala ...nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala +0 -141
- public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala ...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala +0 -361
- public/biopet-extensions/pom.xml public/biopet-extensions/pom.xml +0 -58
- public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py ...umc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py +0 -192
- public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py ...lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py +0 -34
- public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py ...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py +0 -54
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala +0 -40
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala ...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala +0 -63
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala +0 -236
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala +0 -150
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala +0 -38
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala .../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala +0 -240
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala +0 -99
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala +0 -103
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala +0 -206
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala +0 -50
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala +0 -91
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala ...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala +0 -124
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala +0 -63
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala ...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala +0 -74
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala +0 -117
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala +0 -83
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala ...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala +0 -46
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala +0 -138
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala +0 -108
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala +0 -169
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala +0 -115
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/TarExtract.scala +0 -48
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala ...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala +0 -371
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala .../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala +0 -307
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala ...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala +0 -56
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala .../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala +0 -63
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala ...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala +0 -26
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala ...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala +0 -87
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala .../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala +0 -64
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala ...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala +0 -199
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala ...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala +0 -26
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala ...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala +0 -69
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala ...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala +0 -88
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala ...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala +0 -72
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala .../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala +0 -43
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala .../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala +0 -99
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala ...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala +0 -255
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala .../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala +0 -49
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala ...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala +0 -49
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala ...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala +0 -106
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala ...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala +0 -75
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala ...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala +0 -47
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala ...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala +0 -31
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala +0 -101
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala ...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala +0 -59
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala +0 -116
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala ...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala +0 -82
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala ...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala +0 -60
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala .../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala +0 -88
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala ...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala +0 -34
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala .../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala +0 -48
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala .../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala +0 -35
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala ...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala +0 -39
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala .../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala +0 -40
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala ...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala +0 -55
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala ...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala +0 -55
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala ...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala +0 -73
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala ...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala +0 -74
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala ...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala +0 -94
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala .../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala +0 -62
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala ...scala/nl/lumc/sasc/biopet/extensions/gmap/GmapBuild.scala +0 -60
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala ...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala +0 -442
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala ...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala +0 -31
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala .../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala +0 -128
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala .../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala +0 -79
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala .../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala +0 -55
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala ...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala +0 -30
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala .../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala +0 -119
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala ...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala +0 -98
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala .../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala +0 -47
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala .../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala +0 -47
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala ...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala +0 -42
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala ...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala +0 -34
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala ...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala +0 -38
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala ...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala +0 -37
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala ...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala +0 -37
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala ...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala +0 -45
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala ...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala +0 -41
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala ...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala +0 -77
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala .../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala +0 -53
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala .../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala +0 -56
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala .../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala +0 -44
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala .../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala +0 -37
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala ...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala +0 -94
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala ...umc/sasc/biopet/extensions/picard/BedToIntervalList.scala +0 -54
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala ...nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala +0 -39
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala ...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala +0 -91
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala ...et/extensions/picard/CollectAlignmentSummaryMetrics.scala +0 -87
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala .../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala +0 -92
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala ...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala +0 -92
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala ...asc/biopet/extensions/picard/CollectMultipleMetrics.scala +0 -131
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala .../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala +0 -107
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala .../biopet/extensions/picard/CollectTargetedPcrMetrics.scala +0 -94
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala ...umc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala +0 -83
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CreateSequenceDictionary.scala ...c/biopet/extensions/picard/CreateSequenceDictionary.scala +0 -47
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala ...l/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala +0 -36
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala ...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala +0 -116
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala ...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala +0 -78
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala .../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala +0 -166
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala ...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala +0 -59
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala ...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala +0 -104
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala ...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala +0 -62
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala .../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala +0 -220
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala .../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala +0 -97
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala ...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala +0 -110
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala ...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala +0 -102
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala ...a/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala +0 -56
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala ...nl/lumc/sasc/biopet/extensions/qiime/MergeOtuTables.scala +0 -53
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala ...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala +0 -76
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala ...scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala +0 -166
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala ...ala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala +0 -60
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala ...mc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala +0 -96
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala ...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala +0 -31
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala ...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala +0 -40
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala .../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala +0 -60
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala ...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala +0 -67
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala .../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala +0 -43
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala ...l/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala +0 -48
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala .../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala +0 -27
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala ...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala +0 -27
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala .../lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala +0 -49
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala ...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala +0 -42
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala ...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala +0 -85
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala ...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala +0 -52
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala ...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala +0 -70
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala ...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala +0 -27
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala ...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala +0 -126
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala ...a/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala +0 -27
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala ...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala +0 -29
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala ...c/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala +0 -65
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala +0 -28
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala ...scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala +0 -47
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala ...scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala +0 -55
- public/biopet-extensions/src/test/resources/log4j.properties public/biopet-extensions/src/test/resources/log4j.properties +0 -25
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala ...t/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala +0 -50
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala ...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala +0 -52
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala ...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala +0 -44
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala ...rc/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala +0 -126
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala ...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala +0 -387
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala ...c/sasc/biopet/extensions/VariantEffectPredictorTest.scala +0 -50
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala ...xtensions/picard/CollectAlignmentSummaryMetricsTest.scala +0 -40
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala ...opet/extensions/picard/CollectInsertSizeMetricsTest.scala +0 -40
- public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala ...mc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala +0 -40
- public/biopet-public-package/pom.xml public/biopet-public-package/pom.xml +0 -159
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala ...in/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala +0 -45
- public/biopet-public-package/src/test/resources/log4j.properties ...biopet-public-package/src/test/resources/log4j.properties +0 -25
- public/biopet-tools-extensions/pom.xml public/biopet-tools-extensions/pom.xml +0 -67
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala ...la/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala +0 -102
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala ...umc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala +0 -70
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala .../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala +0 -52
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala ...sc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala +0 -38
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala ...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala +0 -57
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala .../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala +0 -43
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala +0 -104
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala ...cala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala +0 -56
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala ...umc/sasc/biopet/extensions/tools/KrakenReportToJson.scala +0 -70
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala ...a/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala +0 -59
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala ...a/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala +0 -40
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala ...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala +0 -100
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala ...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala +0 -78
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala ...la/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala +0 -68
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala ...nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala +0 -38
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala ...lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala +0 -54
- public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala ...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala +0 -54
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